The decision to pool samples in the initial screening PCR reflected logistical constraints, however any saving in cost and time is countered by a loss of diagnostic sensitivity, which becomes particularly problematic when modest amounts of genetic material are present in the samples. In addition, the low level Ebola viral RNA detected from non-invasive swabs has prompted some studies to use tissue samples to maximise the probability of detection in infected bats (e.g., Amman et al. [8]). However, in this study we were constrained from destructively sampling bats, and thus our scope for viral detection may have been reduced. The aim of the study was to identify presence or absence of infection in bat taxa, and an optimistic target sample size was set to allow robust epidemiological interpretation of negative findings. This sample size was not met for any species or genus, and accordingly we refrain from making any interpretation on the lack of detection in any taxa. Conversely, our detection of infection in the modest sample of M. schreibersii indicates that, at the time of the study, infection prevalence was substantially higher than our conservative design prevalence.